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Why Metabolon?

Metabolomics Raw Spectral Data

Metabolomics is a rapidly advancing field that provides valuable insights into the complexity of biological systems. The metabolome, resulting from an individual’s environment and genome, is the closest representation of an organism’s phenotype. Metabolomics has shown great potential in understanding biological processes, advancing drug development, biomarker discovery, environmental research, and precision medicine. However, a significant challenge in untargeted metabolomics remains the comprehensive translation of raw data into the identification (annotation) of metabolites required for valid biological insights.

metabolomics raw spectral data

Insights from Raw Spectral Data

Raw spectral data files are the initial data generated during a mass spectrometry-based metabolomic analysis. They contain a wealth of information about the metabolites present in a sample, including their chemical structure, concentration, and interactions with other molecules. Despite containing thousands of data points, extracting meaningful and biologically relevant information can be difficult as the processing and analysis of these files is time-intensive and requires experience to ensure quality. Additionally, the analysis of the same dataset with different software tools can also yield different results, highlighting the lack of standardization in the still nascent field.

At Metabolon, we have leveraged our 20+ years of experience performing metabolomic analyses to build world-class ML/AI-based software tools to facilitate these processes in a robust and scalable manner. Customers across academia, population health, pharmaceuticals, and biotech send us their samples, and Metabolon provides an end-to-end service from sample extraction to data interpretation. We strive to provide the highest quality metabolomics services available to advance your science by delivering actionable insights from your data.

raw spectral data

As the market leader, our repository of data assets has reached a pivotal level where these resources enable de novo exploration and discovery. These capabilities are integral to providing an in-depth mechanistic understanding of a myriad of diseases, diagnostics, and drug development. This endeavor extends beyond our internal initiatives, encompassing collaborative efforts with our clients who are actively seeking out innovative solutions.

Related Resources

To find out more about metabolomics raw spectral data, take a look at our resources below.

Spectral Data Utilization Guide

Metabolomics utilizes raw spectral data as the primary source of information for identifying and quantifying small molecules (metabolites) present in biological samples.

A Guide for Uploading Metabolon Metabolomic mzML Raw Data to MetaboLights Repository

Read this guide to learn how to upload Metabolon metabolomic mzMl raw data to MetaboLights Repository.

A Guide for Uploading Metabolon Metabolomic mzML Raw Data to Metabolomics Workbench

Read this guide to learn how to upload Metabolon metabolomic mzMl raw data to Metabolomics Workbench.

Frequently Asked Questions

Please read the frequently asked questions for more information about Metabolon’s spectral data deliverable.


What is the spectral data deliverable?

  • The spectral data deliverable provides information about the ions generated and measured from client samples on Metabolon’s LC-MS platform for Global Discovery Panel products.
  • The spectral data deliverable includes scan information from MS1 analysis and MS/MS (MS2) spectral data for ions that underwent tandem mass spectrometry fragmentation analysis.
  • Spectral data can be processed to extract the retention times, mass-to-charge ratios, isotopic distributions, and abundances for ions measured from client samples.
  • The scan data are provided in MZML format, a file format that is ingestible by downstream applications, including many open-source tools designed to work with spectral data.

How does the spectral data deliverable differ from other deliverables, such as the Client Data Table (CDT), for Metabolon’s Global Discovery Panel?

  • Data included in the spectral data deliverable are generated from the same LC-MS platform and passed through the same Platform QC process as the data included in our other Global Discovery Panel deliverables.
  • Whereas other (non-spectral) Global Discovery Panel deliverables include named metabolites (CDT), the spectral data deliverable simply provides information on ions that were measured from the client samples.
  • For non-spectral Global Discovery Panel deliverables, Metabolon uses custom tools to process spectral data into named metabolites with abundances. These non-spectral Global Discovery Panel deliverables can also be used with the Integrated Bioinformatics Platform. The Bioinformatics Platform connects these named metabolites to Metabolon’s custom metabolite knowledge database and tools that enable researchers to leverage Metabolon’s extensive biochemistry experience to advance research objectives.

Do I need the spectral data deliverable for my research program?

  • Spectral data will not be useful for everyone. The Client Data Table, and Integrated Bioinformatics Platform remain the most useful ways to work with metabolomics data from Metabolon.
  • These other (non-spectral) deliverables and tools drive biological insights by providing abundances of named metabolites that enable customers to leverage Metabolon’s extensive biochemical knowledge and experience.
  • Some researchers may like the ion feature information in the spectral data deliverable to meet a raw data requirement for their institution, journal, or funding agency. Other researchers may aim to use the spectral data to mine the features for additional insights beyond those delivered with Metabolon’s deliverables that contain named metabolites.
  • While many publicly available tools can be used to work with spectral data, it is essential to note that using these tools to mine data for additional insights is a challenging bioinformatics endeavor that can yield misleading results if not appropriately evaluated. For this reason, Metabolon has spent two decades expanding our library of Level 1 identifications, refining metabolite annotation software tailored to our platform, and developing a Bioinformatics Platform that delivers biological insights from metabolomics data sets, and we do not endorse any publicly available tools that work with spectral data.
  • Please read below to further assess your need for the Spectral Data Deliverable.
  • Additional information on working with spectral data can be found in our Spectral Data Utilization Guide.

What Metabolon Products offer the spectral data deliverable?

  • The spectral data deliverable is available to request as an additional deliverable with the Global Discovery Panel products with contracts executed in 2024 and beyond.
  • The spectral data deliverable is not available for projects with contracts executed prior to 2024.

How do people work with spectral data in their research programs?

  • Each research program is unique and will have its own way of working with spectral data. Some common uses include data reprocessing, data QC, relative standard deviations (RSD) calculations from technical replicate data, and mining features for further discoveries.
  • Note that Metabolon has already applied rigorous QA and QC protocols to report the named metabolite data included in the other Global Discovery Panel (Client Data Table, Heatmap and Integrated Bioinformatics Pipeline).
  • Several open-source tools are available to work with Spectral Data, as described in our Spectral Data Utilization Guide.
  • Metabolon does not use any of the tools described in the guide or elsewhere.

What are some potential challenges in working with spectral data?

  • Working with spectral data can be very challenging. Data processing steps—from peak picking and feature extraction to compound identification and verification—are all full of challenges and pitfalls that can result in inaccurate data sets if improper tools and expertise are not leveraged.
  • Metabolon developed custom tools, used under rigorous QA and QC protocols, that ensure each of these steps leads to an accurate data set. For that reason, we do not use other tools that are commonly used to work with spectral data.
  • See the Spectral Data Utilization Guide for more information on tools that are available to work with spectral data.

How do I receive the spectral data deliverable?

  • For contracts that include the optional spectral data deliverable, the deliverable will be made available for download in the Client Portal at the time of delivery of the other project deliverables.
  • The spectral data will remain available in the Client Portal for one year after project delivery; after that time, it will move to “cold storage” and can be retrieved for an administrative fee.
  • Note that the spectral data deliverable can have a large data volume (up to 100GB) and may require special accommodations that require planning with support from your IT Team.
  • The Client Portal will contain information on the volume of spectral data for your project so that you can plan accordingly to download and work with the data.

How do I include the spectral data deliverable with my project? What is the fee for the spectral data deliverable?

  • Beginning in 2024, the spectral data deliverable can be added to contracts for Global Discovery Panel products as an additional deliverable for no additional fee.
  • If the original project contract was executed in 2024 (or after), but spectral data was not added as a deliverable in the original contract, clients can obtain the spectral data deliverable via a change order for an administrative fee.
  • Changes to processes and infrastructure were required to enable Metabolon to provide the spectral data. The spectral data deliverable is not available for projects with contracts executed prior to 2024.

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Request a quote for our services, get more information on sample types and handling procedures, request a letter of support, or submit a question about how metabolomics can advance your research.

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